This is a review of key factors for pharmacy and therapeutics committees to consider when developing a therapeutic interchange (TI) program for venous thromboembolism (VTE) prophylaxis. Recent patient safety initiatives aimed at reducing the incidence of hospital-acquired VTE may increase the prescribing of thromboprophylactic agents recommended in VTE management guidelines. As a result, more pharmacy and therapeutics committees may consider TI programs for parenteral anticoagulants. However, the TI of anticoagulants appears challenging at this time. Firstly, the therapeutic equivalence of the commonly prescribed parenteral anticoagulants, enoxaparin, dalteparin and fondaparinux, has not been established. Secondly, because of the wide range of clinical indications for these anticoagulants, a blanket agent-specific TI program could lead to off-label use. Use of an indication-specific TI program could be difficult to manage administratively, and may cause prescribing confusion and errors. Thirdly, careful dosing and contraindications of certain parenteral anticoagulants in special patient populations, such as those with renal impairment, further impact the suitability of these agents for inclusion in TI programs. Finally, although TI may appear to offer lower drug-acquisition costs, it is important to determine its effect on all cost parameters and ultimately ensure that the care of patients requiring VTE prophylaxis is not compromised.